-LRB- CNN -RRB- A murder weapon is n't the only thing missing as prosecutors try to convince jurors that former New England Patriot Aaron Hernandez orchestrated the execution of Odin Lloyd .

The shoes prosecutors say Hernandez was wearing at the industrial park where Lloyd was killed also have seemingly vanished into thin air .

`` The shoes and footprints caused by the shoes -LRB- are -RRB- a big deal , '' says CNN legal analyst Paul Callan , a former homicide prosecutor .

A big deal because connecting an athletic shoe impression found near Lloyd 's body to Hernandez could help prove he directly participated in Lloyd 's death .

Lloyd , 27 , was shot once in the back and six times in the front in June 2013 -- the final two bullets fired as he lay face up , according to the medical examiner . Hernandez has pleaded not guilty .

Aaron Hernandez 's downward spiral

The sneakers prosecutors believe Hernandez wore the night of Lloyd 's death were within the grasp of investigators who visited the ex-football star 's home , but it appears no one knew it at the time .

Investigators photographed a pair of Nike Air Jordan XI Retro Low brand sneakers during one of their first searches of Hernandez 's home , according to court papers , but did not take them in as evidence .

When Lloyd 's body was discovered , crime scene investigators singled out one of two footwear impressions early on because one did n't match the `` lugged sole '' shoes of police , nor the shoes of first responders or civilian witnesses who found Lloyd 's body , according to court documents .

When police began executing search warrants for weapons and clothing at Hernandez 's home on June 18 and June 22 , 2013 , they also were looking for shoes that could match that print in the dirt , according to court files and testimony .

So far , jurors have not been told that somehow three other sets of sneakers neatly lined up side by side along a bedroom wall in the basement were overlooked , and `` appeared to be in good condition , '' according to an affidavit . The basement is where Hernandez 's man cave is located and is complete with bar , a screening room , a pool table with a New England Patriot 's logo , and a trophy room .

That affidavit dated November 14 , 2014 , says that after studying images and home security video and having `` consulted with Nike , '' investigators believe those three pairs of shoes are `` believed to be produced by Nike and Creative Recreation . '' They are the white and black Air Jordan XI Retros , the red Creative Recreation Cesario low tops ; and the brown Nike Air Jordan winterized spike sneakers allegedly worn by Hernandez , Wallace and Ortiz , respectively .

Wallace and Ortiz are also charged with the murder of Lloyd . They have pleaded not guilty and are going to be tried separately .

Wallace and Ortiz are seen on home security video entering the house and going into the basement after getting out of a car minutes after Lloyd was fatally shot in a nearby industrial park . Prosecutors say the cable connecting the basement security camera , labeled `` man cave , '' was unplugged after the three men went downstairs .

Authorities say the `` outsole pattern , '' of the Air Jordan XI Retro Low 's allegedly worn by Hernandez is `` similar to and consistent with the unidentified shoe impression ... in close proximity to the body of Odin Lloyd , '' according to the affidavit . It also states the XI Retro Lows became available for public sale only three weeks before Lloyd 's murder .

Yet , it was n't until almost a year and a half later , when investigators were making final trial preparations last November , that they `` noted '' the three pairs of shoes in photographs and realized they could still be at Hernandez 's home , a search warrant affidavit states .

In court papers , investigators said the sneakers appear to match shoe prints found at the scene where Lloyd was fatally shot .

In order to look again , police asked a court to approve another search warrant . The application also points out home surveillance video showing Wallace and Ortiz leaving the home after the shooting -- wearing sandals .

Trying to make the case for another search , investigators also quote a jailhouse phone call dated December 25 , 2013 , between Hernandez and his fiancee Shayanna Jenkins .

Hernandez told Jenkins , `` You still got my , my clothes at the house and s -- ? ''

Jenkins responded , `` I really do n't understand . I mean , where do you think your clothes are ? ... Your clothes are exactly where they 're supposed to be ... I mean , you 've only been gone for what , six months ? ''

`` Yeah , '' Hernandez said .

`` You act like you 're gon na be gone for like , 20 years , '' Jenkins replied .

But when police searched the home again on November 24 , they did n't find the shoes .

Details about the missing Nike sneakers have not yet come up at trial . How might it play with the jury ?

`` Jurors will wonder why did n't investigators seize the shoes at the same time they seized many other pieces of evidence from Hernandez 's home , '' says University of New Hampshire law professor Michael McCann , who 's closely monitoring the trial .

`` If jurors determine investigators and prosecutors simply made a mistake in not seizing the shoes , it could damage the jurors ' confidence in the case . It 's possible prosecutors could try to mollify this concern by noting that rules of evidence and pretrial discovery limit the types of evidence they can be taken from a person 's home . ''

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Shoes prosecutors say Hernandez wore on night of Lloyd 's death are missing

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Hernandez is on trial for murder of Lloyd and has pleaded not guilty

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Linking shoes to impressions at crime scene would help prosecution with its case